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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Zhang, Y.Z."

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Search Summary

This query matches 31 Structures.

Refinements

Structure Determination Methodology

experimental (31)

Scientific Name of Source Organism

	Saccharomyces cerevisiae S288C (19)
	Saccharomyces cerevisiae (8)
	Homo sapiens (5)
	Schizosaccharomyces pombe (1)
	Schizosaccharomyces pombe 972h- (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (31)
	other sequences (1)

Experimental Method

	ELECTRON MICROSCOPY (24)
	X-RAY DIFFRACTION (7)

Polymer Entity Type

	Protein (31)
	RNA (23)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (1)
	2.5 - 3.0 (7)
	3.0 - 3.5 (10)
	3.5 - 4.0 (9)
	4.0 - 4.5 (2)
	> 4.5 (1)

Release Date

	2010 - 2014 (5)
	2015 - 2019 (18)
	2020 - 2024 (8)

Enzyme Classification Name

	Hydrolases (16)
	Transferases (14)
	Ligases (5)
	Isomerases (3)

Symmetry Type

	Asymmetric (31)
	Cyclic (1)

SCOP Classification

	All beta proteins (8)
	Alpha and beta proteins (a+b) (2)
	Peptides (3)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (2)
	Small proteins (1)
	Coiled coil proteins (1)
	Artifacts (1)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 31 Structures

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3JB9 \| pdb_00003jb9	Download File View File

Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution

Yan, C., Hang, J., Wan, R., Huang, M., Wong, C., Shi, Y.

(2015) Science 349: 1182-1191

Released	2015-09-23
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Schizosaccharomyces pombe Schizosaccharomyces pombe 972h-
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 5
Unique Ligands	ADP, GDP, MG, ZN

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3JCM \| pdb_00003jcm	Download File View File

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP

Wan, R., Yan, C., Bai, R., Wang, L., Huang, M., Wong, C.C., Shi, Y.

(2016) Science 351: 466-475

Released	2016-02-24
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	Unique protein chains: 23 Unique nucleic acid chains: 4
Unique Ligands	GTP, M7M

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4M75 \| pdb_00004m75	Download File View File

Crystal structure of Lsm1-7 complex

Zhou, L., Hang, J., Zhou, Y., Wan, R., Lu, G., Yan, C., Shi, Y.

(2014) Nature 506: 116-120

Released	2013-10-23
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 7
Unique Ligands	CL

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4M77 \| pdb_00004m77	Download File View File

Crystal structure of Lsm2-8 complex, space group I212121

Zhou, L., Hang, J., Zhou, Y., Wan, R., Lu, G., Yan, C., Shi, Y.

(2014) Nature 506: 116-120

Released	2013-11-13
Method	X-RAY DIFFRACTION 3.111 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 7

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4M78 \| pdb_00004m78	Download File View File

Crystal structure of Lsm2-8 complex, space group P21

Zhou, L., Hang, J., Zhou, Y., Wan, R., Lu, G., Yan, C., Shi, Y.

(2014) Nature 506: 116-120

Released	2013-11-13
Method	X-RAY DIFFRACTION 2.794 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 7

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4M7A \| pdb_00004m7a	Download File View File

Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA

Zhou, L., Hang, J., Zhou, Y., Wan, R., Lu, G., Yan, C., Shi, Y.

(2014) Nature 506: 116-120

Released	2013-11-13
Method	X-RAY DIFFRACTION 2.781 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1

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4M7D \| pdb_00004m7d	Download File View File

Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU

Zhou, L., Hang, J., Zhou, Y., Wan, R., Lu, G., Yan, C., Shi, Y.

(2014) Nature 506: 116-120

Released	2013-11-13
Method	X-RAY DIFFRACTION 2.595 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 7 Unique nucleic acid chains: 1

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5GM6 \| pdb_00005gm6	Download File View File

Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution

Yan, C., Wan, R., Bai, R., Huang, G., Shi, Y.

(2016) Science 353: 904-911

Released	2016-09-21
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 38 Unique nucleic acid chains: 5
Unique Ligands	ADP, GTP, MG, ZN

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5GMK \| pdb_00005gmk	Download File View File

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Wan, R., Yan, C., Bai, R., Huang, G., Shi, Y.

(2016) Science 353: 895-904

Released	2016-08-17
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 6
Unique Ligands	GTP, MG, ZN

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5M23 \| pdb_00005m23	Download File View File

Modulation of MLL1 Methyltransferase Activity

Srinivasan, V.

(2017) Chem Sci 8: 4612-4618

Released	2017-06-28
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Homo sapiens
Macromolecule	WD repeat-containing protein 5 (protein)
Unique Ligands	7DC

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5M25 \| pdb_00005m25	Download File View File

Modulation of MLL1 Methyltransferase Activity

Srinivasan, V.

(2017) Chem Sci 8: 4612-4618

Released	2017-06-28
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens
Macromolecule	WD repeat-containing protein 5 (protein)
Unique Ligands	7DU

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5MPS \| pdb_00005mps	Download File View File

Structure of a spliceosome remodeled for exon ligation

Fica, S.M., Oubridge, C., Galej, W.P., Wilkinson, M.E., Newman, A.J., Bai, X.-C., Nagai, K.

(2017) Nature 542: 377-380

Released	2017-01-18
Method	ELECTRON MICROSCOPY 3.85 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 25 Unique nucleic acid chains: 5
Unique Ligands	GTP, IHP, K, MG, ZN

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5MQ0 \| pdb_00005mq0	Download File View File

Structure of a spliceosome remodeled for exon ligation

Fica, S.M., Oubridge, C., Galej, W.P., Wilkinson, M.E., Newman, A.J., Bai, X.-C., Nagai, K.

(2017) Nature 542: 377-380

Released	2017-01-18
Method	ELECTRON MICROSCOPY 4.17 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Unique protein chains: 30 Unique nucleic acid chains: 6
Unique Ligands	GTP, IHP, K, MG, ZN

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5WSG \| pdb_00005wsg	Download File View File

Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution

Yan, C., Wan, R., Bai, R., Huang, G., Shi, Y.

(2017) Science 355: 149-155

Released	2017-01-25
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 7
Unique Ligands	GTP, MG, ZN

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5Y88 \| pdb_00005y88	Download File View File

Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom

Wan, R., Yan, C., Bai, R., Lei, J., Shi, Y.

(2017) Cell 171: 120-132

Released	2018-08-01
Method	ELECTRON MICROSCOPY 3.46 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 5
Unique Ligands	GTP, IHP, MG, ZN

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5YLZ \| pdb_00005ylz	Download File View File

Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom

Wan, R., Yan, C., Bai, R., Lei, J., Shi, Y.

(2017) Cell 171: 1589-1598.e8

Released	2018-07-18
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 4
Unique Ligands	GTP, IHP, MG, ZN

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5ZWM \| pdb_00005zwm	Download File View File

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)

Bai, R., Wan, R., Yan, C., Lei, J., Shi, Y.

(2018) Science 360: 1423-1429

Released	2018-08-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 38 Unique nucleic acid chains: 5
Unique Ligands	GTP, MG, ZN

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5ZWN \| pdb_00005zwn	Download File View File

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.3 angstrom (Part II: U1 snRNP region)

Bai, R., Wan, R., Yan, C., Lei, J., Shi, Y.

(2018) Science 360: 1423-1429

Released	2018-08-29
Method	ELECTRON MICROSCOPY 3.4 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 18 Unique nucleic acid chains: 2
Unique Ligands	ZN

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5ZWO \| pdb_00005zwo	Download File View File

Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom

Bai, R., Wan, R., Yan, C., Shi, Y.

(2018) Science 360: 1423-1429

Released	2018-08-29
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 41 Unique nucleic acid chains: 5
Unique Ligands	GTP, MG

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6J6G \| pdb_00006j6g	Download File View File

Cryo-EM structure of the yeast B*-a2 complex at an average resolution of 3.2 angstrom

Wan, R., Bai, R., Yan, C., Lei, J., Shi, Y.

(2019) Cell 177: 339-351.e13

Released	2019-04-24
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 27 Unique nucleic acid chains: 4
Unique Ligands	GTP, IHP, MG, ZN

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6J6H \| pdb_00006j6h	Download File View File

Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom

Wan, R., Bai, R., Yan, C., Lei, J., Shi, Y.

(2019) Cell 177: 339-351.e13

Released	2019-04-24
Method	ELECTRON MICROSCOPY 3.6 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 27 Unique nucleic acid chains: 4
Unique Ligands	GTP, IHP, MG, ZN

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6J6N \| pdb_00006j6n	Download File View File

Cryo-EM structure of the yeast B*-b1 complex at an average resolution of 3.86 angstrom

Wan, R., Bai, R., Yan, C., Lei, J., Shi, Y.

(2019) Cell 177: 339-351.e13

Released	2019-04-24
Method	ELECTRON MICROSCOPY 3.86 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 27 Unique nucleic acid chains: 4
Unique Ligands	GTP, IHP, MG, ZN

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6J6Q \| pdb_00006j6q	Download File View File

Cryo-EM structure of the yeast B*-b2 complex at an average resolution of 3.7 angstrom

Wan, R., Bai, R., Yan, C., Lei, J., Shi, Y.

(2019) Cell 177: 339-351.e13

Released	2019-04-24
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 28 Unique nucleic acid chains: 4
Unique Ligands	GTP, IHP, MG, ZN

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7DCO \| pdb_00007dco	Download File View File

Cryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom

Bai, R., Wan, R., Yan, C., Qi, J., Zhang, P., Lei, J., Shi, Y.

(2021) Science 371:

Released	2021-03-17
Method	ELECTRON MICROSCOPY 2.5 Å
Organisms	Saccharomyces cerevisiae Saccharomyces cerevisiae S288C
Macromolecule	Unique protein chains: 43 Unique nucleic acid chains: 4
Unique Ligands	CA, GTP, IHP, MG, ZN

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7DCP \| pdb_00007dcp	Download File View File

cryo-EM structure of the DEAH-box helicase Prp2 and coactivator Spp2

Bai, R., Wan, R., Yan, C., Jia, Q., Zhang, P., Lei, J., Shi, Y.

(2021) Science 371:

Released	2021-01-06
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	PRP2 isoform 1 (protein) Pre-mRNA-splicing factor SPP2 (protein)
Unique Ligands	ADP, MG

1 to 25 of 31 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3JB9 | pdb_00003jb9

3JCM | pdb_00003jcm

4M75 | pdb_00004m75

4M77 | pdb_00004m77

4M78 | pdb_00004m78

4M7A | pdb_00004m7a

4M7D | pdb_00004m7d

5GM6 | pdb_00005gm6

5GMK | pdb_00005gmk

5M23 | pdb_00005m23

5M25 | pdb_00005m25

5MPS | pdb_00005mps

5MQ0 | pdb_00005mq0

5WSG | pdb_00005wsg

5Y88 | pdb_00005y88

5YLZ | pdb_00005ylz

5ZWM | pdb_00005zwm

5ZWN | pdb_00005zwn

5ZWO | pdb_00005zwo

6J6G | pdb_00006j6g

6J6H | pdb_00006j6h

6J6N | pdb_00006j6n

6J6Q | pdb_00006j6q

7DCO | pdb_00007dco

7DCP | pdb_00007dcp